ZNF41

zinc finger protein 41, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:47445178-47483222

Links

ENSG00000147124 ∙ NCBI:7592 ∙ OMIM:314995 ∙ HGNC:13107 ∙ Uniprot:P51814 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic X-linked intellectual disability (Disputed Evidence), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mental retardation, X-linked 89	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	14628291; 23871722
The evidence of variants as being related to disease causation has been questioned due to subsequent population-based studies

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF41 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF41 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	6	3	10
missense			35	5	7	47
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	40	12	10

Variants in ZNF41

This is a list of pathogenic ClinVar variants found in the ZNF41 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-47447438-T-A		not specified	Uncertain significance (Mar 20, 2023)
X-47447461-C-G			Likely benign (Nov 01, 2022)
X-47447463-A-G		not specified	Likely benign (Sep 06, 2019)
X-47447477-G-A		not specified	Uncertain significance (Apr 23, 2024)
X-47447555-T-A		History of neurodevelopmental disorder	Uncertain significance (Dec 01, 2010)
X-47447626-C-T		not specified	Uncertain significance (Aug 22, 2023)
X-47447650-T-C		not specified	Uncertain significance (Jul 25, 2023)
X-47447656-C-T		History of neurodevelopmental disorder	Conflicting classifications of pathogenicity (Jan 01, 2023)
X-47447657-G-T		not specified	Uncertain significance (Apr 01, 2024)
X-47447766-A-G		not specified	Likely benign (Jun 29, 2019)
X-47447773-G-A		History of neurodevelopmental disorder	Benign (Apr 28, 2016)
X-47447899-G-A		not specified	Uncertain significance (Jun 23, 2021)
X-47447911-G-A		not specified	Uncertain significance (Nov 17, 2023)
X-47447938-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-47447950-T-A		not specified	Uncertain significance (Mar 20, 2024)
X-47447974-C-A		not specified	Uncertain significance (Mar 28, 2024)
X-47448038-G-A		not specified	Uncertain significance (Aug 08, 2023)
X-47448065-G-T		not specified	Uncertain significance (Dec 19, 2023)
X-47448076-C-T		not specified	Uncertain significance (Apr 12, 2022)
X-47448077-G-A		not specified	Conflicting classifications of pathogenicity (Apr 01, 2022)
X-47448079-G-A		not specified	Uncertain significance (Jan 24, 2024)
X-47448173-TA-T			Uncertain significance (Mar 10, 2022)
X-47448192-A-T		not specified	Benign (Jan 22, 2016)
X-47448225-T-C			Uncertain significance (Jan 16, 2013)
X-47448468-C-T		not specified	Likely benign (Nov 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF41	protein_coding	protein_coding	ENST00000377065	4	37068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0351	0.963	125727	4	12	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	229	292	0.785	0.0000213	5206
Missense in Polyphen		69	104.7	0.65902		1946
Synonymous	0.383	100	105	0.952	0.00000812	1361
Loss of Function	2.78	6	19.1	0.313	0.00000128	413

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000340	0.000283
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000110	0.0000791
Middle Eastern	0.0000722	0.0000544
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.27

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.148
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.316

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding